rs2070767
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000406213.1(MIF-AS1):n.626A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 802,300 control chromosomes in the GnomAD database, including 243,932 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.78 ( 46334 hom., cov: 30)
Exomes 𝑓: 0.78 ( 197598 hom. )
Consequence
MIF-AS1
ENST00000406213.1 non_coding_transcript_exon
ENST00000406213.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.309
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIF-AS1 | NR_038911.1 | n.626A>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIF-AS1 | ENST00000406213.1 | n.626A>G | non_coding_transcript_exon_variant | 3/3 | 1 | |||||
ENSG00000290199 | ENST00000703580.1 | n.1221A>G | non_coding_transcript_exon_variant | 4/4 | ||||||
MIF | ENST00000465752.1 | n.*49T>C | downstream_gene_variant | 1 | ||||||
MIF | ENST00000498385.1 | n.*49T>C | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.781 AC: 118618AN: 151868Hom.: 46290 Cov.: 30
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GnomAD3 exomes AF: 0.784 AC: 115256AN: 146996Hom.: 45290 AF XY: 0.784 AC XY: 62212AN XY: 79326
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GnomAD4 exome AF: 0.778 AC: 505886AN: 650314Hom.: 197598 Cov.: 8 AF XY: 0.779 AC XY: 269411AN XY: 345700
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GnomAD4 genome AF: 0.781 AC: 118716AN: 151986Hom.: 46334 Cov.: 30 AF XY: 0.784 AC XY: 58229AN XY: 74296
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at